I'm trying to merge an alignment to a reference sequence and a de novo assembly using the same Illumina reads. It seems like minimus2 would be the right tool for the job, but every time I run it I get no overlaps and all the sequences just dump into singletons.seq. Just as a test, I tried assembling the alignment contigs to themselves (i.e. made a file with two copies of the alignment contigs, then performed alignment with minimus2) and again got no overlaps and all singletons!
I'm already a little wary of this program since I had to go in and modify it for myself just to get it to run (I kept getting usage errors on dumpreads steps 12 and 13 until I moved $(BANK) after the -m/M options instead of before), but that's the only change I made. Is there some other glitch I don't know about?
Any suggestions?
Full disclosure: I didn't install qt3 when I installed amos since it wouldn't compile on OSX 10.6, but my impression is that's just for the viewers and minimus shouldn't depend on it.
Thanks.
I'm already a little wary of this program since I had to go in and modify it for myself just to get it to run (I kept getting usage errors on dumpreads steps 12 and 13 until I moved $(BANK) after the -m/M options instead of before), but that's the only change I made. Is there some other glitch I don't know about?
Any suggestions?
Full disclosure: I didn't install qt3 when I installed amos since it wouldn't compile on OSX 10.6, but my impression is that's just for the viewers and minimus shouldn't depend on it.
Thanks.
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